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Gray Team was formed from the three SPARTAN-II candidates who were the most difficult to control during training. This manifested in consistent resistance to indoctrination, constant attempts to escape training, and significant lack of social integration. This disruptive behavior was costly, resulted in injuries to trainers, and the theft and destruction of at least one Pelican dropship. The decision was subsequently made to train the trio separately from the rest and form them into their own unit.

Compared to the standard SPARTAN-IIs, Gray Team's training placed additional emphasis on individual thought and action. This made them suitable to execute and survive covert missions deep behind enemy lines, of their own accord, with no backup. Their assignments focused on disruption of enemy operations followed by a stealthy extraction.

The Cole Protocol was implemented to slow the Covenant advance by denying them navigational information of UNSC space. Some insurrectionist enclaves survived the Covenant advance by remaining hidden; these rebels did not fall under UNSC jurisdiction and had no obligation to honor the Cole Protocol. In 2535, Gray Team was sent to locate and infiltrate these enclaves and enforce the Cole Protocol by purging the navigation databases of any rebel ships they found. This led to the Battle of the Rubble. Gray Team aided the Rubble under the command of LieutenantJacob Keyes and participated in the Battle of Metisette, which led to the destruction of the majority of Covenant forces in the area. With the help of the UNSC Midsummer Night and her crew, they completed their mission in the system and returned to UNSC-controlled space on the Midsummer Night. There they asked for another ONIProwler, having abandoned their freighter, the Petya. They were given a Prowler and assigned a new mission deeper behind enemy lines and farther from UNSC forces, which they happily accepted.

In 2551, Gray Team was deemed too inaccessible to be recalled to Reach. They were not present when the Covenant invaded the planet, having been out of contact for about a year.[2] Gray Team were the only operational SPARTAN-IIs not present at the Fall of Reach and did not receive the Mark V Mjolnir Armor.[3][4]